convert2annovar.pl -format rsid T1D.txt -dbsnpfile humandb/hg19_snp138.txt > T1D_MS_formatted
## V1 V2 V3 V4 V5 V6
## 1 chr6 29692305 29692305 A G rs1632953
## 2 chr6 29694427 29694427 C T rs1059174
## 3 chr6 29696209 29696209 G A rs1736921
## 4 chr6 29704083 29704083 C T rs1736916
## 5 chr6 29704400 29704400 T C rs1736913
## 6 chr6 29708222 29708222 T C rs1610603
## [1] "rs6931717" "rs7452756" "rs12199773" "rs6937967" "rs12178292"
## [6] "rs10456058" "rs7382662" "rs10807118" "rs10947377"
missing SNP IDs were renamed from PUBMED
rs6931717 > rs3095345
rs7452756 > rs4516988
rs12199773 > rs3130952
rs6937967 > rs3130534
rs12178292 > rs2844558
rs10456058 > rs2734573
rs7382662 > rs3129305
rs10807118 > rs3130578
rs10947377 > rs3130179Created a new file T1D_2.txt after chainging SNP ids
Rerun in ANNOVAR and obtained results for all 119 SNPs
## V1 V2 V3 V4 V5 V6
## 1 chr6 29692305 29692305 A G rs1632953
## 2 chr6 29694427 29694427 C T rs1059174
## 3 chr6 29696209 29696209 G A rs1736921
## 4 chr6 29704083 29704083 C T rs1736916
## 5 chr6 29704400 29704400 T C rs1736913
## 6 chr6 29708222 29708222 T C rs1610603
## Genomic region Gene Chromosome BP_1 BP_2 A1 A2 SNP
## 1 intronic HLA-F chr6 29692305 29692305 A G rs1632953
## 2 ncRNA_exonic HLA-F-AS1 chr6 29694427 29694427 C T rs1059174
## 3 ncRNA_exonic HLA-F-AS1 chr6 29696209 29696209 G A rs1736921
## 4 ncRNA_exonic HLA-F-AS1 chr6 29704083 29704083 C T rs1736916
## 5 ncRNA_exonic HLA-F-AS1 chr6 29704400 29704400 T C rs1736913
## 6 ncRNA_intronic HLA-F-AS1 chr6 29708222 29708222 T C rs1610603
## Genomic region Gene Chromosome BP_1 BP_2 A1 A2 SNP
## 1 intronic ENSG00000204642 chr6 29692305 29692305 A G rs1632953
## 2 ncRNA_exonic ENSG00000214922 chr6 29694427 29694427 C T rs1059174
## 3 ncRNA_exonic ENSG00000214922 chr6 29696209 29696209 G A rs1736921
## 4 ncRNA_exonic ENSG00000214922 chr6 29704083 29704083 C T rs1736916
## 5 ncRNA_exonic ENSG00000214922 chr6 29704400 29704400 T C rs1736913
## 6 ncRNA_intronic ENSG00000214922 chr6 29708222 29708222 T C rs1610603
## Genomic_region Gene Chromosome BP_1 BP_2 A1 A2 SNP
## 1 intronic HLA-F chr6 29692305 29692305 A G rs1632953
## 2 ncRNA_exonic HLA-F-AS1 chr6 29694427 29694427 C T rs1059174
## 3 ncRNA_exonic HLA-F-AS1 chr6 29696209 29696209 G A rs1736921
## 4 ncRNA_intronic HLA-F-AS1 chr6 29704083 29704083 C T rs1736916
## 5 ncRNA_intronic HLA-F-AS1 chr6 29704400 29704400 T C rs1736913
## 6 ncRNA_intronic HLA-F-AS1 chr6 29708222 29708222 T C rs1610603